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| BLASTZ, LASTZ
| Seeded pattern-matching || Nucleotide || Local || Schwartz ''et al.''<ref>{{Cite journal| author=Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W| title=Human-mouse alignments with BLASTZ| journal=Genome Research |volume=13 |issue=1 |date=2003 |pages=103–107 |pmid=12529312 | pmc=430961| doi=10.1101/gr.809403| last2=Kent| last3=Smit| last4=Zhang| last5=Baertsch| last6=Hardison| last7=Haussler| last8=Miller}}</ref><ref>{{Cite thesis| author=Harris R S | year=2007| title=Improved pairwise alignment of genomic DNA}}</ref> || 2004,2009
|-
| [[CodonCode Aligner]]
| Fast pairwise and multi-sequence alignments with multiple algorithms. || Nucleotide || Both || CodonCode Corporation || 2003-2025
|-
| CUDAlign
| |||